Serine-threonine kinase gene

ABSTRACT

A novel gene having the consensus sequence of a serine-threonine kinase active site has been isolated by the suppression subtractive hybridization method which comprised of preparing a library of genes expressed specifically in fetal livers and isolating clones from this library at random. This gene presumably participates in cell growth control because it is highly expressed, especially in actively growing cells, and exhibits a significant homology with a vaccinia virus B1R kinase gene. Thus, it can be utilized as a target for developing cell growth inhibitors or antitumor agents.

This application is a divisional application of and claims priority under 35 USC §120 of U.S. application Ser. No. 09/563,997, filed on May 3, 2000, now U.S. Pat. No. 6,677,437, which is a divisional application of and claims priority under 35 USC §120 of U.S. application Ser. No. 09/344,700, filed on Jun. 25, 1999, now U.S. Pat. No. 6,265,194, which is a continuation-in-part of International Application PCT/JP97-04855 filed Dec. 25, 1997, which claims priority from Japanese Patent Application No. 8/357864 filed Dec. 27, 1996.

TECHNICAL FIELD

The present invention relates to a novel serine-threonine kinase gene.

BACKGROUND OF ART

Fetal tissues are comprised of many undifferentiated cells that proliferate actively, highly activated cells, nascent vascular endothelial cells, and so on. Although the activity of these cells in fetal tissues is stringently regulated and inhibited as individuals mature, the state of fetal tissues can be considered similar to that of a solid tumor except that the activity is regulated. Therefore, some of the genes expressed specifically or more strongly in fetal tissues (fetal genes) can be genes involved in the phenomena characteristic of solid tumors such as abnormal growth, immortalization, infiltration, metastasis, and angiogenesis. In addition, some diseases other than tumors are also supposed to arise because fetal genes, which are repressed in a normal living body, are abnormally activated. Therefore, genes involved in various diseases such as tumors can be screened by isolating and analyzing fetal genes.

However, there are still few reports on systematic analysis focusing merely on fetal genes from these viewpoints, and at present there is a far from perfect understanding of these gene groups.

DISCLOSURE OF THE INVENTION

An objective of this invention is to isolate genes expressed specifically in fetal tissues and to screen genes related to diseases.

The present inventors thought that fetal tissue cells could be a model for solid tumor cells and that genes involved in diseases such as tumors could be screened by isolating and analyzing fetal genes. Furthermore, the present inventors thought it possible to develop a medicine with a novel action mechanism by designing drugs targeting the genes. Based on these thoughts, the present inventors have tried to isolate fetal genes.

Specifically, the present inventors prepared a subtraction library with many genes expressed specifically in fetal livers (or more strongly than adult livers) by the suppression subtractive hybridization method, extracted clones from this library at random, and analyzed their structure. By doing so, the present inventors succeeded in isolating a novel gene, VRK1, having the consensus sequence of a serine-threonine kinase active site. The present inventors also performed a data base search based on the amino acid sequence deduced from the isolated gene. The present inventors thus have found this gene product exhibits a significant homology with B1R kinase, which is presumably involved in DNA replication of vaccinia virus. In addition, the present inventors found human EST having a very high homology with this gene in the database and isolated its full-length cDNA, VRK2. Analyzing the expression of the two isolated genes in various cells by northern blot analysis showed that these genes are strongly expressed, especially in actively growing cells such as human fetal livers, testes, and various tumor cell lines. Furthermore, the present inventors have found that the VRK1 protein actually has protein kinase activity.

Thus, the present invention relates to novel serine-threonine kinase genes, VRK1 and VRK2. More specifically, the present invention relate to:

-   (1) a protein having the amino acid sequence of SEQ ID NO: 2, or a     protein having the same amino acid sequence where one or more amino     acids are added, deleted, or substituted and having serine-threonine     kinase activity, -   (2) a protein having the amino acid sequence of SEQ ID NO: 4, or a     protein having the same amino acid sequence where one or more amino     acids are added, deleted, or substituted and having serine-threonine     kinase activity, -   (3) a protein encoded by a DNA sequence that hybridizes with the DNA     sequence of SEQ ID NO: 1 or its complementary sequence and having     serine-threonine kinase activity, -   (4) a protein encoded by a DNA sequence that hybridizes with the DNA     sequence of SEQ ID NO: 3 or its complementary sequence and having     serine-threonine kinase activity, -   (5) a DNA encoding the protein of any one of (1) to (4), -   (6) a vector comprising the DNA of (5), -   (7) a transformant carrying the vector of (6), -   (8) a method of producing the protein of any one of (1) to (4),     wherein the method comprises cultivating the transformant of (7), -   (9) an antibody binding to the protein of any one of (1) to (4), -   (10) an antisense DNA against the DNA of (5) or part of it, -   (11) a method of screening compounds having inhibitory activity of     serine-threonine kinase activity of the protein of any one of (1) to     (4), wherein the method is comprised of -   (a) contacting the protein of any one of (1) to (4) with a substrate     to be phosphorylated by this protein in the presence of a test     compound to detect the kinase activity of the protein of any one     of (1) to (4), and -   (b) comparing the kinase activity detected in step (a) with that     detected in the absence of the test compound and selecting a     compound that lowers the kinase activity of the protein of any one     of (1) to (4).

The present invention relates to novel serine-threonine kinases, “VRK1” and “VRK2.” The nucleotide sequence of the “VRK1” cDNA and the amino acid sequence of the protein are shown in SEQ ID NO: 1 and 2, respectively. In addition, the nucleotide sequence of the “VRK2” cDNA and the amino acid sequence of the protein are shown in SEQ ID NO: 3 and 4, respectively. “VRK1” cDNA has a significant homology with B1R kinase, which is presumably involved in DNA replication of vaccinia virus. The gene is also characterized by its strong expression in actively growing cells such as fetal livers, testes, and various tumor cell lines. In addition, overexpression of “VRK1” protein drastically increases the growing activity of NIH3T3 cells. These facts imply “VRK1” is involved in the regulation mechanism of cell growth. “VRK1” protein has protein kinase activity, which presumably plays an important roll in the regulation of cell growth. “VRK2” has a high homology with “VRK1,” especially in the serine-threonine kinase site. “VRK2,” like “VRK1,” has a significant homology with B1R kinase, and the gene is characterized by its strong expression in actively growing cells such as fetal livers, testes, and various tumor cell lines. These facts imply “VRK2” has the same function as that of “VRK1.”

“VRK1” and “VRK2” proteins can be prepared as recombinant proteins with recombinant DNA techniques or as natural proteins. The recombinant proteins can be prepared, for example, by cultivating cells transformed with the DNAs encoding these proteins, as will be described later. Natural proteins can be isolated from fetal livers, testes, or tumor cell strains such as HeLa S3, in which these proteins are highly expressed, by a method well-known to one skilled in the art, such as affinity chromatography with the antibodies of the present invention as described later. Either polyclonal or monoclonal antibodies can be used. The polyclonal antibodies can be prepared from, for example, serum from small animals such as rabbits immunized with these proteins by, for example, ammonium sulfate precipitation, protein A- or protein G-column chromatography, DEAE ion exchange chromatography, affinity chromatography using a column coupled with these proteins, etc. The monoclonal antibodies can be prepared as follows. First, a small animal such as a mouse is immunized with these proteins. The spleen is extracted from the mouse and dissociated to cells. The resulting cells are fused to mouse myeloma cells using a reagent such as polyethylene glycol, and the clone that produces antibodies against these proteins is screened from the fusion cells (hybridoma) thus generated. The hybridoma thus obtained is then transplanted into a mouse abdominal cavity. Ascites is collected from the mouse and purified by, for example, ammonium sulfate precipitation, protein A- or protein G-column chromatography, DEAE ion exchange chromatography, affinity chromatography using a column coupled with “VRK1” or “VRK2” protein, etc. If the antibodies obtained are to be used for administering to a human body (for antibody therapy or the like, etc.), humanized antibodies or human antibodies should be used to decrease immunogenicity. An example of methods for humanizing antibodies is the CDR graft method, in which an antibody gene is cloned from monoclonal antibody-producing cells and its antigenic determinant is transplanted to an existing human antibody. Besides, human antibodies can be directly prepared just like usual monoclonal antibodies by immunizing a mouse whose immune system is replaced with a human immune system.

Furthermore, one skilled in the art can prepare not only natural “VRK1” and “VRK2” proteins (SEQ ID NO: 2 and 4, respectively) but also proteins with substantially the same function as that of the natural proteins, if needed, by replacing amino acids in the proteins by a well-known method. Besides, mutations of amino acids in proteins can occur naturally. Thus, mutant proteins with serine-threonine kinase activity that are generated by introducing amino acid substitution, deletion, or addition into the natural proteins are also included in the proteins of the present invention. Methods for amino acid alteration, for example, a site-directed mutagenesis system using PCR (GIBCO-BRL, Gaithersburg, Maryland), the oligonucleotide-mediated site-directed mutagenesis method (Kramer, W. and Fritz, H J (1987) Methods in Enzymol., 154:350–367), and the Kunkel method (Methods Enzymol. 85, 2763–2766 (1988)), are well-known to one skilled in the art. Furthermore, usually ten or less, preferably six or less, and more preferably three or less amino acids are substituted. For example, proteins functionally equivalent to the VRK1 or VRK2 protein can be produced by conservative amino acid substitutions at one or more amino acid residues. A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, s leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). The site where substitution, deletion, or addition is introduced is not particularly limited as long as the serine-threonine kinase activity is maintained. From the viewpoint of protein activity, the addition, deletion, or substitution of amino acids should be performed in a region other than the region corresponding to the consensus sequence of a serine-threonine kinase active site and to the consensus sequence of a protein kinase ATP binding site. Moreover, serine-threonine kinase activity of a protein can be detected, for example, by the method described in Example 9, mentioned later.

Furthermore, one skilled in the art can usually isolate DNAs having a high homology with the DNA encoding “VRK1” or “VRK2” protein (SEQ ID NO: 1 or 3, respectively) based on the DNA or the part of it using a hybridization technique (Sambrook, J. et al., Molecular Cloning 2nd ed. 9.47–9.58, Cold Spring Harbor Lab. Press, 1989) and obtain proteins having substantially the same function as VRK1 or VRK2 protein (SEQ ID NO: 2 or 4, respectively) from the DNA. Thus, proteins with serine-threonine kinase activity that are encoded by DNAs hybridizing with DNA encoding “VRK1” or “VRK2” protein are also included in the proteins of the present invention. Hybridizing DNAs are isolated from other organisms including, for example, mice, rats, rabbits, and bovines, and so on . Tissues such as fetal livers and testes are especially suitable for isolating. Thus isolated DNAs encoding proteins having substantially the same function as that of “VRK1” or “VRK2” proteins usually have a high homology with the DNA (SEQ ID NO: 1 or 3) encoding “VRK1” or “VRK2” protein, respectively. The term “high homology” used herein means at least 40% or more, preferably 60% or more, and more preferably 80% or more of sequence identity at the amino acid level. From the viewpoint of the protein activity, a high homology should be found in the regions corresponding to the consensus sequence of a serine-threonine kinase active site and to the consensus sequence of a protein kinase ATP binding site.

To determine the percent homology of two amino acid sequences or of two nucleic acids, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino or nucleic acid sequence) . The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent homology between the two sequences is a function of the number of identical positions shared by the sequences (i.e., % identity=# of identical positions/total # of positions (e.g., overlapping positions)×100). In one embodiment the two sequences are the same length.

To determine percent homology between two sequences, the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264–2268, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873–5877 is used. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul, et al. (1990) J. Mol. Biol. 215:403–410. BLAST nucleotide searches are performed with the NBLAST program, score=100, wordlength=12 to obtain nucleotide sequences homologous to a nucleic acid molecule of the invention. BLAST protein searches are performed with the XBLAST program, score=50, wordlength=3 to obtain amino acid sequences homologous to a VRK1 or VRK2 protein molecules. To obtain gapped alignments for comparison purposes, Gapped BLAST is utilized as described in Altschul et al. (1997) Nucleic Acids Res. 25:3389–3402. When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST) are used. See the website at ncbi.nlm.nih.gov.

Furthermore, the present invention relates to a DNA that specifically hybridizes under moderate or highly stringent conditions to a DNA encoding a protein of the present invention and comprises at least 15 nucleotide residues. The DNA can be used, for example, as a probe to detect or isolate a DNA encoding a protein of the present invention, or as a primer for PCR amplification. An example is DNA consisting of at least 15 nucleotides complementary to the nucleotide sequence of SEQ ID NO: 2 or NO: 3.

Standard hybridization conditions (e.g., moderate or highly stringent conditions) are known to those skilled in the art and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1–6.3.6, hereby incorporated by reference. Moderate hybridization conditions are defined as equivalent to hybridization in 2× sodium chloride/sodium citrate (SSC) at 30° C., followed by one or more washes in 1×SSC, 0.1% SDS at 50–60° C. Highly stringent conditions are defined as equivalent to hybridization in 6× sodium chloride/sodium citrate (SSC) at 45° C., followed by one or more washes in 0.2×SSC, 0.1% SDS at 50–65° C.

Examples of conditions for hybridization to isolate these DNAs are as follows. After prehybridization at 55° C. for 30 minutes or longer, hybridization is performed by adding labeled probes and incubating at 37° C. to 55° C. for an hour or longer using “ExpressHyb Hybridization Solution” (CLONTECH). After that, the resulting hybridized products are washed three times for 20 minutes each at room temperature in 2×SSC and 0.1% SDS then once at 37° C. in 1×SSC and 0.1% SDS. More preferably, after prehybridization at 60° C. for 30 minutes or longer, hybridization is performed by adding labeled probes and incubating at 60° C. for an hour or longer using “ExpressHyb Hybridization Solution” (CLONTECH). Thereafter, the hybridized products are washed three times for 20 minutes each at room temperature in 2×SSC and 0.1% SDS then twice at 50° C. in 1×SSC and 0.1% SDS. Still more preferably, after prehybridization at 60° C. for 30 minutes or longer, hybridization is performed by adding labeled probes and incubating at 68° C. for an hour or longer using “ExpressHyb Hybridization Solution” (CLONTECH). Thereafter, the hybridized product is are washed three times for 20 minutes each at room temperature in 2×SSC and 0.1% SDS then twice at 50° C. in 0.1×SSC and 0.1% SDS.

The present invention also relates to the DNAs encoding the above-described proteins of the present invention. The DNAs of the present invention include cDNAs, genomic DNAs, and synthetic DNAs as long as they encode the proteins of the present invention. The DNAs of the present invention can be used to produce the recombinant proteins. Specifically, the recombinant proteins can be prepared by inserting the DNA (for example, the DNA of SEQ ID NO: 1 or 3) of the present invention into a suitable expression vector, cultivating the transformant obtained by introducing the vector into suitable cells, and purifying the expressed proteins. For example, mammalian cells such as COS, CHO, or NIH3T3 cells; insect cells such as Sf9 cells; yeast cells; and E. coli cells can be used for producing the recombinant proteins. Vectors for expressing recombinant proteins in these cells vary depending on the host cells. For example, pcDNA3 (Invitrogen) or pEF-BOS (Nucleic Acids. Res. 1990, 18(17), p5322) is used for mammalian cells; “BAC-to-BAC baculovirus expression system” (GIBCO BRL), for insect cells; “Pichia Expression Kit” (Invitrogen), for yeast cells; and pGEX-5X-1 (Pharmacia) or “QIAexpress system” (Qiagen), for E. coli cells. Vectors can be introduced into host cells by, for example, the method using calcium phosphate, DEAE dextran, or cationic liposome DOTAP (Boehringer Mannheim); electroporation; the calcium chloride method; etc. The recombinant proteins can be purified from the obtained transformants by the usual methods such as the method described in “The Qiaexpressionist handbook, Qiagen, Hilden, Germany.”

Furthermore, the DNAs of the present invention can be used for gene therapy of diseases caused by mutations in genomic DNAs. In gene therapy, the DNAs of the present invention are administered to a living body inserted into adenovirus vectors (e.g., pAdexLcw), retrovirus vectors (e.g., pZIPneo) and so on. They can be administered by either ex vivo methods or in vivo methods.

Furthermore, since the proteins of the present invention are presumably involved in the regulation of cell growth, antisense DNAs against the DNAs of the present invention or part of them can be used as inhibitors for developing cell growth or as antitumor agents. The antisense DNAs are administered to a living body directly or in the form of the vectors into which they have been inserted. The antisense DNAs can be synthesized by methods well known to one skilled in the art.

The present invention also relates to a method of screening compounds having inhibitory activity of serine-threonine kinase activity of the proteins of the present invention. This screening method consists of two steps. First, the protein of the present invention is caused to contact a substrate to be phosphorylated by this protein in the presence of a test compound to detect the kinase activity of the protein of the present invention. Second, the kinase activity detected in step (a) is compared with that detected in the absence of the test compound, and a compound that lowers the kinase activity of the protein of the present invention is selected.

Test compounds used for this screening method are not particularly limited and are generally low-molecular-weight compounds, proteins (including the above-described antibodies of the present invention), peptides, etc. Test compounds are either artificially synthesized or natural. Substrates are, for example, casein, IkBα protein, etc. The kinase activity of the protein of the present invention can be detected, for example, by adding ATP having radioactively labeled phosphate to the reaction system containing the protein of the present invention and the substrate and measuring the radioactivity of the phosphate attached to the substrate. Specifically, the activity is detected by the method described in Example 9. The compounds thus isolated can be used as cell growth inhibitors or antitumor agents. Moreover, the present inventors learned that “VRK1” protein phosphorylates IkBα protein. IkBα is thought to be rapidly degraded when phosphorylated, thereby releasing and activating NF-kB bound thereto. In addition, NF-kB is well known as a central transcriptional regulator that causes widespread immune reactions and inflammation reactions. Therefore, compounds that inhibit the kinase activity of the proteins of the present invention can be used as antiphlogistics and immunosuppressants.

BRIEF DESCRIPTION OF THE DRAWING

FIG. 1 shows adapter 1 (SEQ ID NOs: 38 and 39) and adapter 2 (SEQ ID NOs: 40 and 41) used for constructing the subtraction library.

FIG. 2A shows the consensus sequence of the active site of serine-threonine kinase (SEQ ID NO:49).

FIG. 2B shows the consensus sequence of the ATP binding site of protein kinase (SEQ ID NO:50).

FIG. 3 shows the nucleotide sequence of the clone fls223 (SEQ ID NOs: 42, 44, and 46) and its deduced amino acid sequences (Frame 1—SEQ ID NO: 43: Frame 2—SEQ ID NO: 45; Frame 3—SEQ ID NO: 47).

FIG. 4 shows electrophoretic patterns demonstrating the result of RT-PCR analysis performed to detect expressions of VRK1 and VRK2 genes in fetal and adult livers. In the figure, “A” and “F” represent Adult liver, and Fetal liver. “Low,” “Middle,” and “High” represent the level of PCR cycles.

FIG. 5 compares amino acid sequences of VRK1 (SEQ ID NO: 2) and B1R (SEQ ID NO: 48).

FIG. 6 compares amino acid sequences of VRK1 (SEQ ID NO: 2) and VRK2 (SEQ ID NO: 4).

FIG. 7 compares amino acid sequences of VRK2 (SEQ ID NO: 4) and B1R (SEQ ID NO: 48).

FIG. 8 shows electrophoretic patterns demonstrating the result of northern blot analysis of the expression of VRK1 and VRK2 genes in various cells.

FIG. 9 shows an electrophoretic pattern demonstrating the result of western blot analysis using anti c-Myc antibody. Cell extracts from COS7 cells transfected with plasmid DNA, pcDNA3 (lane 1) or pcDNA3/VRK1myc (lane 2), were examined.

FIG. 10 shows an electrophoretic pattern demonstrating the result of northern blot analysis using the VRK1 cDNA as a probe. Total RNA samples prepared from NIH3T3 cells transfected with plasmid DNA, pCOS (lane 1) or pCOS/VRK1w (lane 2), and from a human hepatoma cell line, HepG2 cells (lane 3), were examined.

FIG. 11 presents microscopic photographs showing the result of colony assay. A pool of NIH3T3 cells transfected with plasmid DNA, pCOS (“pCOS”) or pCOS/VRK1w (“pCOS/VRK1w”) was examined.

FIG. 12 shows an electrophoretic pattern of purified GST fusion proteins (CBB staining). Fusion proteins with wild VRK1 protein (lane 1) or with a mutant one (lane 2) were examined.

FIG. 13 shows electrophoretic patterns demonstrating the result of kinase assay. Added proteins are indicated by “+” on the upper portion. Arrows indicate phosphorylated GST-VRK1 (“A,” autophosphorylation), phosphorylated casein (“C”), phosphorylated GST-IkBα (“I”), and phosphorylated IkBα C-terminal peptide (“P”).

FIG. 14 shows an electrophoretic pattern demonstrating the result of kinase assay. Reactions were performed in the presence of various divalent cations at various concentrations as indicated on the right. Arrows indicate phosphorylated GST-VRK1 (“A,” autophosphorylation), and phosphorylated casein (“C”).

FIG. 15 shows an electrophoretic pattern demonstrating the result of western blot analysis with an antibody against a VRK1 peptide using K562 cell extracts.

DETAILED DESCRIPTION OF THE INVENTION

The present invention is illustrated below in detail with reference to examples, but is not to be construed as being limited thereto.

EXAMPLE 1

Construction of a Subtraction Library

A subtraction library was prepared using the PCR-Select™ cDNA Subtraction kit (CLONTECH) basically according to the method described by Luda Diatchenko et al. (Proc. Natl. Acad. Sci. USA, Vol. 93, 6025–6030, 1996).

First, double-stranded cDNAs were synthesized from polyA⁺ RNA prepared from human fetal and adult livers by the standard method using MMLV reverse transcriptase. Next, the respective cDNAs were blunt-ended with T4 DNA polymerase, then cleaved by RsaI. A part of the cDNA originating from fetal liver (tester) was split in two; one of which was ligated with the adapter-1 and the other with the adapter-2 (FIG. 1). Each aliquot was mixed with an excess amount of the adult liver cDNA (driver), denatured by heat, and subjected to the first hybridization at 68° C. for 8 hours. Aliquots were then combined without heat denaturation, mixed further with an excess amount of heat-denatured driver, and subjected to the second hybridization at 68° C. for about 16 hours. The mixture was diluted in the dilution buffer, incubated at 75° C. for 7 minutes to remove the shorter strands of adapters, and used as a template for PCR. By performing PCR with primers corresponding to the adapters, “PCR primer-1” (SEQ ID NO: 5) and “PCR primer-2” (SEQ ID NO: 6), cDNAs carrying different adapters on their two ends (subtracted cDNAs) were selectively amplified (suppression PCR). To obtain products with further selectivity, a portion of the amplified products was used as a template for PCR with primers “Nested PCR primer-1” (SEQ ID NO: 7) and “Nested PCR primer-2” (SEQ ID NO: 8), which locate further inside of the primers; “PCR primer-1” (SEQ ID NO: 5); and “PCR primer-2” (SEQ ID NO: 6). The products were purified using the “QIAquick PCR Purification kit” (QIAGEN), and cloned into the pT7Blue-T vector (Novagen) by the TA cloning method to create a subtraction library.

EXAMPLE 2

Sequence Analysis

Plasmid DNA prepared by the alkali SDS method or products of colony PCR were used as a template for sequence reaction. Sequence reaction was performed by the cycle-sequencing method using the ABI PRISM™ Dye Terminator Cycle Sequencing Ready Reaction Kit With AmplyTaq DNA Polymerase, FS, and the result was analyzed by the ABI 377 DNA Sequencer.

Colony PCR was performed as follows. Colonies carrying recombinant vectors were directly suspended into PCR reaction mixtures that contain vector primers, “M13 P4–22 primer” (SEQ ID NO: 9) and “M13 P5–22 primer” (SEQ ID NO: 10). After PCR reaction, amplified insert DNA was separated from unreacted primers and nucleotides by gel filtration or the like, and used as a template for sequencing.

As a result, the clone fls223 (261 bp) (later renamed “VRK1”) was found to be able to encode an amino acid sequence (FIG. 3) that contains the consensus sequence of the active site of serine-threonine kinase ([Leu, Ile, Val, Met, Phe, Tyr, Cys]-Xaa-[His, Tyr]-Xaa-Asp-[Leu, Ile, Val, Met, Phe, Tyr]-Lys-Xaa-Xaa-Asn-[Leu, Ile, Val, Met, Phe, Tyr, Cys, Thr]-[Leu, Ile, Val, Met, Phe, Tyr, Cys, Thr]-[Leu, Ile, Val, Met, Phe, Tyr, Cys, Thr]) (corresponds to amino acids at 173–185 of SEQ ID NO: 2) (FIG. 2A). In addition, no gene registered in the database completely matches the nucleotide sequence of this clone. Thus, the gene is a novel one.

EXAMPLE 3

RT-PCR Assay

Using polyA⁺ RNA extracted from fetal and adult livers, single-stranded cDNAs wee synthesized by the standard method with SUPERSCRIPT™ II RNase H⁻ Reverse Transcriptase (GIBCO BRL). Some of the cDNAs were used as a template for RT-PCR analysis of fls223. PCR was performed using TaKaRa Taa (TaKaRa) as Taq polymerase by the hot-start method, where the reaction was started by adding TaqStart™ Antibody (CLONTECH). Primers “FLS223 S1 primer” (SEQ ID NO: 11) and “FLS223 A1 primer” (SEQ ID NO: 12) were used to amplify fls22.

The G3PDH (glyceraldehyde 3-phosphate dehydrogenase) gene, which is a housekeeping gene equally expressed in various tissues and known to be influenced only slightly by various inducers on its expression, was used as a control. G3PDH was amplified using the primers “hG3PDH5′ primer” (SEQ ID NO: 13) and “hG3PDH3′ primer” (SEQ ID NO: 14). RT-PCR analysis confirmed that the clone fls223 is strongly expressed in fetal liver, and its expression was also detected in adult liver (FIG. 4). The full-length cDNA was then cloned for more detailed analysis of the gene.

EXAMPLE 4

Cloning by Rapid Amplification of cDNA End (RACE)

The Marathon™ Ready cDNA (CLONTECH) or cDNA prepared by the Marathon™ cDNA Amplification Kit (CLONTECH) was used as a template for 5′ RACE and 3′ RACE (Chenchik A. et al., CLONTECHniques X, 1, 5–8, 1995).

The primers described above, “FLS223 S1 primer” (SEQ ID NO: 11) and “FLS223 A1 primer” (SEQ ID NO: 12), were used for 5′ RACE and 3′ RACE of VRK1/fls223. The reaction, performed with a combination of these primers and a primer AP1 (SEQ ID NO: 15), corresponding to the adapter of the template cDNA, basically consisted of a reaction at 94° C. for (30 seconds) and at 68° C. (4 minutes); and 30 cycles of reactions at 94° C. for (30 seconds), 62° C. for (1 minute), and 72° C. for (3 minutes;) and followed by a reaction at 72° C. for 10 minutes. TaKaRa Ex Taq (TaKaRa) was used for PCR, and the reaction was started by the hot-start method by adding TaqStart™ Antibody (CLONTECH). After the reaction, detected bands were recovered using the QIAquick Gel Extraction Kit (QIAGEN), and subcloned into the pT7Blue-T vector (Novagen).

Analysis of the entire nucleotide sequence revealed that the full-length fls223 cDNA encodes an open reading frame composed of 396 amino acids (refer to SEQ ID NO: 1). In the former part of the amino acid sequence, there exists a consensus sequence of the ATP binding site of protein kinase ([Leu, Ile, Val]-Gly-Xaa-Gly-Xaa-[Phe, Tyr, Trp, Met, Gly, Ser, Thr, Asn, His]-[Ser, Gly, Ala]-Xaa-[Leu, Ile, Val, Cys, Ala, Thr]-Xaa-Xaa-[Gly, Ser, Thr, Ala, Cys, Leu, Ile, Val, Met, Phe, Tyr]-Xaa(five times or 18 times)-[Leu, Ile, Val, Met, Phe, Tyr, Trp, Cys, Ser, Thr, Ala, Arg]-[Ala, Ile, Val, Pro]-[Leu, Ile, Val, Met, Phe, Ala, Gly, Cys, Lys, Arg]-Lys) (corresponds to the amino acids 43–71 described in the SEQ ID NO: 2) (FIG. 2B), and a consensus sequence of the active site of serine-threonine kinase, which is also found in the original clone. Thus, the gene product is assumed to be a novel serine-threonine kinase.

A homology search of the whole database revealed that the gene shows high homology to the B1R gene product of the Vaccinia virus (J. Gen. Virol., 70, 3187–3201, 1989; J. Gen. Virol., 72, 1349–1376, 1991) (FIG. 5). The B1R gene encodes a protein composed of 300 amino acids and is assumed to be a serine-threonine kinase because the gene contains the consensus sequences analogous to that of the ATP binding site of protein kinase and of the active site of serine-threonine kinase. The full-length fls223 cDNA and the B1R gene showed relatively high homology over the entire region as well as in the kinase domain (Smallest Sum probability in Blast search=2.7e−78). Therefore, the gene is named “Vaccinia virus B1R kinase related Kinase 1” (VRK1).

B1R kinase is an early gene whose expression is observed in early stages. It appears several hours after vaccinia virus infection and is then repressed. It has been shown that in a mutant strain containing a point mutation on the gene, virus replication stops during DNA replication. Thus, it has been hypothesized that B1R kinase regulates virus DNA replication (J. Biol. Chem., 264, 21458–21461, 1989).

VRK1 also exhibits an obvious homology to B1R kinase in the region outside of the serine-threonine kinase domain. Thus, VRK1 may participate in the regulation of cellular DNA replication or, more widely, in cell growth control, as is the case for B1R kinase in virus. This notion is supported by the fact that the VRK1 genes are more strongly expressed in tissues such as fetal liver and the testis, where numerous actively growing cells exist.

Furthermore, a public clone “human EST—H80169,” which has an extremely high homology to VRK1, was found by searching the data base. Using the primers “RK A2 primer” (SEQ ID NO: 16) and “RK S1 primer” (SEQ ID NO: 17) for 5′ RACE and 3′ RACE, the full-length cDNA of the gene was cloned as described for VRK1, and the entire nucleotide sequence was determined. As a result, it was found that the gene encodes an open reading frame composed of 508 amino acids (refer to SEQ ID NO: 3), in which the consensus sequence of the active site of serine-threonine kinase exists. Thus, this gene may also encode a novel serine-threonine kinase. The amino acid sequence has an extremely high homology to VRK1, especially near the kinase domain (FIG. 6), and a high homology to the vaccinia virus B1R kinase (FIG. 7). These suggest a close relationship between this kinase and B1R kinase. Thus, it was named “Vaccinia virus B1R kinase related Kinase 2” (VRK2).

RT-PCR confirmed that VRK2 is also expressed more strongly in fetal liver than in adult liver (FIG. 4). The primers “RK S2 primer” (SEQ ID NO: 18) and “RK A2 primer” (SEQ ID NO: 16) were used for RT-PCR.

EXAMPLE 5

Chromosome Mapping

Chromosome mapping of the VRK1 and VRK2 genes was performed using the GENEBRIDGE 4 Radiation Hybrid Panel (Research Genetics, Inc.) (Nature Genetics, 7, 22–28, 1994). DNA on the panel was used as a template for PCR. For VRK1, PCR was performed with a combination of the above primers (“FLS223 S1 primer” (SEQ ID NO: 9) and “FLS223 A1 primer” (SEQ ID NO: 12)) by a reaction at 94° C. for (5 minutes); five cycles of reactions at 94° C. for (30 seconds) and at 72° C. for (2 minutes); and 30 cycles of reactions at 94° C. for (30 seconds) and at 68° C. for (2 minutes; and). This was followed by a reaction at 72° C. for 3 minutes. For VRK2, PCR was performed with a combination of primers “VRK2 A primer” (SEQ ID NO: 19) and “VRK2 B primer” (SEQ ID NO: 20) by a reaction at 94° C. for (3 minutes);, and 30 cycles of reactions at 94° C. for (30 seconds), 60° C. for (1 minute), and 72° C. for (2 minutes; and). This was followed by a reaction at 72° C. for 5 minutes. The resulting pattern was analyzed on an internet database (located at genome.wi.mit.edu/cgi-bin/contig/rhmapper.pl) and maps were obtained.

The VRK1 gene was thus mapped to the position between the STS markers “D14S265” and “AFM063XE7” on chromosome 14. Similarly, the VRK2 gene was mapped to the position between the STS markers “CHLC.GATA23H01” and “D2S357” on chromosome 2.

EXAMPLE 6

Northern Blot Analysis

The expressions of VRK1 and VRK2 mRNA in various human normal tissues and tumor cell lines were analyzed by northern blotting (FIG. 8).

The 5′ terminal fragment of the VRK1 cDNA (upstream region of the HindIII site at nucleotide residue 546) or that of the VRK2 cDNA (upstream region of the EcoRI site at position 426) was labeled with [α-³²P]dCTP by the random primer method using Ready-to-Go DNA labeling beads (Pharmacia), and used as a probe. Hybridization was performed at 68° C. in ExpressHyb Hybridization Solution (CLONTECH) using Multiple Tissue Northern (MTN) Blot-Human, Human II, Human Fetal II, and Human Cell line (CLONTECH) according to the method recommended by the manufacturer. Final wash was done at 50° C. in 0.1×SSC, 0.1% SDS, and the image on the filter processed through hybridization was analyzed with the BAS-2000II bioimaging analyzer (Fuji Photo Film).

In FIG. 8, tumor cell lines used are malignant melanoma cells “G361,” lung carcinoma cells “A549,” colorectal adenocarcinoma cells “SW480,” Burkitt's lymphoma cells “Raji,” acute lymphoblastic leukemia cells (T cell) “MOLT-4,” chronic myelogenous leukemia cells “K-562,” uterocervical carcinoma cells “HeLaS3,” and promyelocytic leukemia cells “HL60”.

The results revealed that VRK1 was expressed relatively highly in fetal tissues, and extremely highly in fetal liver. VRK1 was expressed weakly in almost all adult tissues, but it was expressed strongly in the testis and the thymus. In tumor cell lines, a very strong expression of VRK1 was observed in six out of eight cell lines.

The expression pattern of VRK2 was basically similar to that of VRK1; VRK2 was expressed strongly in fetal liver and the testis. Similarly, it was expressed strongly in tumor cell lines. However, VRK2 was not expressed in MOLT-4 cells, in contrast to the pattern of VRK1 MRNA.

EXAMPLE 7

Constructing Expression Plasmid DNAs

CDNA containing the entire coding region of VRK1 or VRK2 was amplified by PCR using a combination of primers, VRK1 S1 primer (SEQ ID NO: 21) and VRK1 A1 primer (SEQ ID NO: 22), or VRK2 S1 primer (SEQ ID NO: 23) and VRK2 A1 primer (SEQ ID NO: 24) from CDNA synthesized from polyA⁺ RNA extracted from human fetal liver. The amplified product was cleaved at the NotI site that is attached to the end of the primers and purified by agarose gel electrophoresis to obtain DNA fragments of the correct size. These were subcloned into the PCOS vector, which was pretreated with NotI and dephosphorylated on its ends with alkaline-phosphatase/CIAP (TaKaRa). This vector contains an EF1α promoter and enables expressing cloned CDNA strongly in a broad range of mammalian cell lines. By sequencing the thus-obtained subclones, clones (PCOS/VRK1w, PCOS/VRK2w) without mutation such as PCR error were selected and used for expression as described below and for further construction of expression plasmid DNA.

Plasmids for expressing proteins in which the anti c-Myc antibody epitope sequence (SEQ ID NO: 25) is attached to the C-terminus were constructed as follows. Using about 50 nanograms of the plasmid DNA and with PCOS/VRK1w or PCOS/VRK2w as a template, PCR was performed with a combination of primers. These included VRK1 MYC1 primer (SEQ ID NO: 26) and VRK1 MYC2 primer (SEQ ID NO: 27), or VRK2 MYC1 primer (SEQ ID NO: 28) and VRK2 MYC2 primer (SEQ ID NO: 29), and CDNA with the anti c-Myc antibody epitope attached to the C-terminus of the coding sequence was amplified. KOD DNA polymerase (TOYOBO) was used as the DNA polymerase. The amplified product was cleaved at the BamHI site that is attached to the end of the primers and purified by agarose gel electrophoresis to obtain DNA fragments of the correct size. These were subcloned into the pcdna3 vector (Invitrogen), which was digested with BamHI and dephosphorylated on its ends with alkaline-phosphatase/CIAP (TaKaRa). By sequencing the thus-obtained subclones, clones (pcdna3/VRK1myc, pcdna3/VRK2myc) without mutation such as PCR error were selected, and used for later experiments.

Expression plasmid DNAs for glutathione-S-transferase (GST) fusion proteins in E. coli were constructed as follows. Using the plasmid DNA PCOS/VRK1w or PCOS/VRK2w as a template, the coding region was amplified by PCR with a combination of primers, VRK1 H3 primer (SEQ ID NO: 30) and VRK1 H4 primer (SEQ ID NO: 31), or VRK2 H3 primer (SEQ ID NO: 32) and VRK2 H4 primer (SEQ ID NO: 33). The amplified product was cleaved at the BamHI site that is attached to the end of the primers purified by agarose gel electrophoresis to obtain DNA fragments of the correct size. These were then subcloned into the PGEX-5X-1 vector (Pharmacia), which was digested with BamHI and dephosphorylated on its ends with alkaline-phosphatase/CIAP (TaKaRa) . By sequencing the thus-obtained subclones, clones (PGEX/VRK1w, PGEX/VRK2w) without mutation such as PCR error were selected and used for later experiments.

A clone with a mutation introduced to the predicted ATP binding site within the kinase catalytic domain (Lys at position 71 in the amino acid sequence of SEQ ID NO: 2 is replaced by Trp) was constructed using the Chameleon™ Double-Stranded Site-Directed Mutagenesis Kit (STRATAGENE) as follows. About one microgram of the PGEX/VRK1w plasmid DNA was mixed with primers VRK1 KW1 primer (SEQ ID NO: 34) and a selection primer, Select1 primer (SEQ ID NO: 35), and heat denatured by boiling for 5 minutes. Plasmid DNA and both primers containing mutation were then annealed by incubating at room temperature for 30 minutes. Next, new DNA strands were synthesized from primers by adding substrate nucleotides, DNA polymerase, etc. These were treated with PstI to digest wild plasmid DNA, and introduced into XLmutS competent cells. After overnight liquid culture, plasmid DNA was extracted then treated with PstI to digest contaminating wild plasmid DNA. It was then reintroduced into the competent cells. By sequencing several single isolated colonies, a clone (PGEX/VRK1K71W) with an introduced mutation was selected.

EXAMPLE 8

Expression in Mammalian Cell Lines

About 10 micrograms of plasmid DNA, pcdna3/VRK1myc or pcdna3, was introduced (transfected) into COS7 cells using SuperFect (QIAGEN). Specifically, about 10⁶ COS7 cells were plated in a 10-cm dish, and cultured overnight. A mixture of 10 micrograms of plasmid DNA and 60 microliters of SuperFect was then added to the culture, and the culture was incubated for about 3 hours. Thereafter, the culture medium was replaced with fresh medium. The cells were then cultured for two more days and collected by detaching in a trypsin-EDTA solution. Cells were washed once in PBS, disrupted in RIPA buffer (1% NP-40, 10 Mm Tris-Hcl (Ph 7.2), 0.1% sodium deoxychorate, 0.1% SDS, 0.15 M sodium chloride, 1 Mm EDTA, 10 micrograms/ml aprotinin, 1 Mm PMSF), and cell extracts were obtained by centrifugation. The cell extracts were separated by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and subjected to western blot analysis using anti c-Myc antibody (SANTA CRUZ). A band of about 50 kDa was specifically observed in cells transfected with the pcdna3/VRK1myc plasmid DNA, indicating that VRK1myc protein is expressed (FIG. 9).

Next, about 7.5 micrograms of plasmid DNA, PCOS/VRK1w or PCOS, was transfected into NIH3T3 cells by the method using cationic phospholipid DOTAP (Boehringer Mannheim). After transfection, transformants were selected by adding G418 (GIBCO-BRL) to the culture medium to a final concentration of 500 micrograms/ml. Total RNA was prepared from each pool of transformants by the method using ISOGEN (Wako Junyaku). The total RNA was then subjected to northern blot analysis using the VRK1 CDNA as a probe. The results confirmed that VRK1 MRNA was expressed in a pool of cells obtained by transfection with the PCOS/VRK1w plasmid DNA (FIG. 10). These pools of cells were examined for the ability to form colonies on soft agar (colony assay). To this end, 2×10⁴ cells were suspended in Dulbecco's Modified Eagle Medium (DMEM) containing 10% fetal bovine serum and 0.4% thawed SeaPlaque agarose (TaKaRa), and overlaid on a bottom agarose, which was made of 0.53% SeaPlaque agarose, 10% fetal bovine serum, and DMEM. After two-week culturing, the pool of cells obtained by transfection with the PCOS/VRK1w plasmid DNA formed a number of colonies that were obviously larger than those formed in the pool of cells obtained by transfection with the Pcos plasmid DNA. This suggests that overexpression of VRK1 confers abnormal growth activities on cells (FIG. 11).

EXAMPLE 9

Expression of VRK1 Protein in E. coli and Kinase Assay

Both wild VRK1 protein and mutant VRK1 protein were expressed in E. coli as a fusion protein with GST protein and purified. The E. coli DH5α strain cells carrying the above-described plasmid DNA, PGEX/VRK1w, or PGEX/VRK1K71W were cultured overnight at 37° C. in 10 ml 2×YT medium. Some of the culture was diluted 100-fold with fresh 2×YT medium and cultured at 37° C. until the OD value at 600 nm reached 0.6. IPTG (isopropyl-β-D(−)-thiogalactopyranoside) was then added to the culture to a final concentration of 0.1 Mm, and the culture was incubated further for several hours. The E. coli cells were collected by centrifugation, resuspended in PBS containing 1% Triton X-100 and 1% Tween 20, and subsequently disrupted by sonication to solubilize proteins. From the solubilized samples, wild VRK1 protein and mutant VRK1, which were expressed as a fusion protein with GST, were purified by affinity chromatography using glutathione Sepharose4B (Pharmacia). These proteins were subjected to SDS-PAGE and stained with Coomassie Brilliant Blue (CBB) to confirm their purity (FIG. 12). GST protein and GST-IkBα protein were prepared in the same manner.

Kinase assay was performed on a total of 50 microliters of a reaction mixture containing 0.2 micrograms of wild or mutant VRK1 protein, 50 mM Tris-Hcl (Ph 7.2), 1 mM dithiothreitol (DTT), 2 mM or 10 mM of divalent cation (Mg, Mn, Zn, Ca), a maximum of 5 micrograms of substrate protein, and 1 microliter of [γ-³²P]-ATP (3000 Ci/mM, 10 mCi/ml [Amersham]). In some experiments, another buffer system containing 40 mM Hepes (Ph 7.4), 1 mM DTT, and 2.5 mM EGTA was used.

Specifically, the reaction was first performed in the presence of 10 mM Mg at 37° C. for 30 minutes using, as a protein substrate, histone (Nakalai), casein (Sigma), myelin basic protein/MBP (Sigma), GST, GST-IkBα, or IkBα C-terminal peptide (SEQ ID NO: 36). The reaction mixture was subjected to SDS-PAGE, and the radioactivity of phosphorylated proteins was analyzed with a BAS2000II bioimaging analyzer (Fuji Photo Film) . The result indicates that wild VRK1 protein phosphorylates casein and GST-IkBα (FIG. 13). In contrast, no phosphorylation was observed in reactions with mutant VRK1 carrying a mutation in the predicted ATP binding site. This indicates that VRK1 is a protein kinase that contains a typical catalytic domain. In addition, GST protein was not phosphorylated by VRK1, suggesting that the phosphorylation of GST-IkBα protein by VRK1 occurs within GST-IkBα protein but not in the GST moiety.

IkBα is said to negatively regulate the function of transcription factor NF-Kb by forming a complex with it. In addition, it is widely accepted that IkBα is inactivated by self-phosphorylation, immediately thereafter undergoes proteolysis, thereby liberating and activating NF-Kb. NF-Kb is supposed to be a central transcriptional regulator that induces a broad range of immune reactions and inflammatory reactions. Therefore, a kinase that phosphorylates IkBα is important as a target molecule of anti-inflammatory drugs. Since VRK1 strongly phosphorylates IkBα in vitro, VRK1 probably participates in the activation of NF-Kb by phosphorylating IkBα in vivo as well. Therefore, it is possible to anticipate anti-inflammatory effects or immunosuppressive effects by inhibiting VRK1 kinase activity, or by reducing its protein amount.

Next, the requirement for divalent cations in phosphorylation by VRK1 was examined (FIG. 14). In the presence of various divalent cations (Mg, Mn, Zn, and Ca) at a final concentration of 2 mM or 10 mM, kinase reactions were performed using casein as a substrate protein. The result showed that VRK1 exhibits phosphorylation activity in the presence of all divalent cations except for Zn. However, the levels of activity were different; VRK1 exhibited especially strong activity in the presence of Mn.

EXAMPLE 10

Preparation of an Antibody Against VRK1 Protein

A peptide (SEQ ID NO: 37) corresponding to the C-terminal sequence of the deduced VRK1 amino acid sequence was synthesized (Sawady Technology) and conjugated to Keyhole limpet hemocyanin (KLH) at its amino-terminal cysteine mediated by m-maleimidobenzoyl-N-hydroxy-succinimide ester (MBS). This was used as an antigen to immunize rabbits, and antisera were obtained. Antibodies that specifically react with the peptide were purified from the antisera by affinity chromatography using Cellulofine (Seikagaku Corporation) conjugated with the peptide. Western blot analysis using extracts of K562 cells, which were confirmed by northern blot analysis to strongly express VRK1, detected a single band with a molecular weight of approximately 50 Kda, indicating that VRK1 protein is specifically recognized by the antibody (FIG. 15).

INDUSTRIAL APPLICABILITY

The serine-threonine kinase genes isolated by the present inventors show significant homology to a vaccinia virus gene that is thought to be involved in DNA replication and are strongly expressed in actively growing cells. Furthermore, overexpression of proteins encoded by the genes remarkably enhances cell proliferation activity. Thus, the isolated serine-threonine kinase genes are assumed to participate in the regulation of cell growth. Therefore, it is possible to develop cell growth inhibitors or antitumor agents based on a novel mechanism by screening drugs targeted on the genes (such as antisense DNA), or drugs which can regulate either the expression of the genes or the activity of the proteins encoded by the genes of the present invention. 

1. A purified protein comprising the amino acid sequence of SEQ ID NO:2.
 2. The purified protein of claim 1, wherein the protein's amino acid sequence consists of the amino acid sequence of SEQ ID NO:2.
 3. A purified protein comprising the amino acid sequence of SEQ ID NO:4.
 4. The purified protein of claim 3, wherein the protein's amino acid sequence consists of the amino acid sequence of SEQ ID NO:4.
 5. A purified protein having serine-threonine kinase activity, wherein the protein is encoded by a DNA sequence that hybridizes with a DNA probe consisting of the complement of SEQ ID NO:1, under hybridization conditions of incubating at 68° C. for an hour, followed by washing 3 times for 20 minutes each at room temperature in 2×SSC and 0.1% SDS and twice at 50° C. in 0.1×SSC and 0.1% SDS.
 6. A purified protein having serine-threonine kinase activity, wherein the protein is encoded by a DNA sequence that hybridizes with a DNA probe consisting of the complement of SEQ ID NO:3, under hybridization conditions of incubating at 68° C. for an hour, followed by washing 3 times for 20 minutes each at room temperature in 2×SSC and 0.1% SDS and twice at 50° C. in 0.1×SSC and 0.1% SDS. 